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<title>GenomeTools - manual page for GT-INLINESEQ_ADD(1)</title>
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<div class="sect1">
<h2 id="_name">NAME</h2>
<div class="sectionbody">
<div class="paragraph"><p>gt-inlineseq_add - Adds inline sequences from external source to GFF3 input.</p></div>
</div>
</div>
<div class="sect1">
<h2 id="_synopsis">SYNOPSIS</h2>
<div class="sectionbody">
<div class="paragraph"><p><strong>gt inlineseq_add</strong> [options] [GFF3_file &#8230;]</p></div>
</div>
</div>
<div class="sect1">
<h2 id="_description">DESCRIPTION</h2>
<div class="sectionbody">
<div class="dlist"><dl>
<dt class="hdlist1">
<strong>-seqfile</strong> [<em>filename</em>]
</dt>
<dd>
<p>
set the sequence file from which to take the sequences (default: undefined)
</p>
</dd>
<dt class="hdlist1">
<strong>-encseq</strong> [<em>filename</em>]
</dt>
<dd>
<p>
set the encoded sequence indexname from which to take the sequences (default: undefined)
</p>
</dd>
<dt class="hdlist1">
<strong>-seqfiles</strong> 
</dt>
<dd>
<p>
set the sequence files from which to extract the features
use <em>--</em> to terminate the list of sequence files
</p>
</dd>
<dt class="hdlist1">
<strong>-matchdesc</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
search the sequence descriptions from the input files for the desired sequence IDs (in GFF3), reporting the first match (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-matchdescstart</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
exactly match the sequence descriptions from the input files for the desired sequence IDs (in GFF3) from the beginning to the first whitespace (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-usedesc</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
use sequence descriptions to map the sequence IDs (in GFF3) to actual sequence entries.
If a description contains a sequence range (e.g., III:1000001..2000000), the first  part is used as sequence ID (<em>III</em>) and the first range position as offset (<em>1000001</em>) (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-regionmapping</strong> [<em>string</em>]
</dt>
<dd>
<p>
set file containing sequence-region to sequence file mapping (default: undefined)
</p>
</dd>
<dt class="hdlist1">
<strong>-o</strong> [<em>filename</em>]
</dt>
<dd>
<p>
redirect output to specified file (default: undefined)
</p>
</dd>
<dt class="hdlist1">
<strong>-gzip</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
write gzip compressed output file (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-bzip2</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
write bzip2 compressed output file (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-force</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
force writing to output file (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-help</strong> 
</dt>
<dd>
<p>
display help and exit
</p>
</dd>
<dt class="hdlist1">
<strong>-version</strong> 
</dt>
<dd>
<p>
display version information and exit
</p>
</dd>
</dl></div>
</div>
</div>
<div class="sect1">
<h2 id="_reporting_bugs">REPORTING BUGS</h2>
<div class="sectionbody">
<div class="paragraph"><p>Report bugs to <a href="https://github.com/genometools/genometools/issues">https://github.com/genometools/genometools/issues</a>.</p></div>
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